Another boolean modifier problem
From my experience it seams, that when using boolean you should always make ends of hole cutting mesh, stick out of the mesh, that is being cut. So in this instance you have to go to edit mod and raise up top vertices of bolts, above surface of window clip and lower bottom vertices of bolts below surface of window clip. This will solve the problem.
p.s.
By bolts I mean cutouts, lift nuts and cutouts, glue plugs